taf3  (Proteintech)

Journal: Oncology Letters

Article Title: Identification of a novel FOXO3‑associated prognostic model in hepatocellular carcinoma

doi: 10.3892/ol.2025.14976

Figure Lengend Snippet: Identification of the 5-gene signature. (A) Forest plot of univariate Cox regression analysis in The Cancer Genome Atlas dataset. Cox results for the top five and bottom five genes. (B) Least absolute shrinkage and selection operator regression analysis. (C) λ curves show the least absolute shrinkage and the best λ was selected based on the minimum criteria. (D) The protein-protein interaction network between FOXO3 and 294 genes. FOXO3, DDX55, RAB10, RAB7A, TAF1B and TAF3 are highlighted by red dots and the remaining genes are represented by green dots. The color of the edges was determined by the combined score obtained from STRING. FOXO3, Forkhead box O3; DDX55, DEAD-box helicase 55; RAB10, RAB10, member RAS oncogene family; RAB7A, RAB7A, member RAS oncogene family; TAF1B, TATA-box binding protein associated factor, RNA polymerase I subunit B; TAF3, TATA-box binding protein associated factor 3; SLC4A1AP, solute carrier family 4 member 1 adaptor protein; ZNF765, zinc finger protein 765; MORC3, MORC family CW-type zinc finger 3; WWC2, WW and C2 domain containing 2; UBE3A, ubiquitin protein ligase E3A; SECISBP2L, SECIS binding protein 2 like; FAN1, FANCD2 And FANCI associated nuclease 1.

Article Snippet: The following antibodies were used: β-actin (1:1,000; cat. no. ET1702-52; HUABIO), DDX55 (1:1,000; cat. no. ER63225; HUABIO), RAB10 (1:1,000; cat. no. 11808-1-AP; Proteintech Group, Inc.), RAB7A (1:1,500; cat. no. 55469-1-AP; Proteintech Group, Inc.), TAF1B (1:500; cat. no. 12818-1-AP; Proteintech Group, Inc.), FOXO3 (1:1,000; cat. no. A9270; ABclonal Biotech Co., Ltd.) and TAF3 (1:500; cat. no. 18901-1-AP; Proteintech Group, Inc.), HRP conjugated goat anti-rabbit IgG polyclonal antibody (1:30000, HA1001, HUABIO), HRP conjugated goat anti-mouse IgG polyclonal antibody (1:30,000, HA1006, HUABIO).

Techniques: Selection, Binding Assay, Ubiquitin Proteomics

Journal: Oncology Letters

Article Title: Identification of a novel FOXO3‑associated prognostic model in hepatocellular carcinoma

doi: 10.3892/ol.2025.14976

Figure Lengend Snippet: Construction and validation of a 5-gene prognostic model. (A) The distribution of RS, survival status and expression of the 5-gene signature between the high- and low-risk groups in TCGA dataset. (B) Overall survival of patients with HCC in the high- and low- RS groups in TCGA dataset. (C) Time-dependent ROC curve of RS in TCGA dataset. (D) The distribution of RS, survival status and expression of the 5-gene signature between the high- and low-risk groups in the ICGC dataset. (E) Overall survival of patients with HCC in the high- and low-RS groups in the ICGC dataset. (F) Time-dependent ROC curve of RS in the ICGC dataset. RS, risk score; TCGA, The Cancer Genome Atlas; ICGC, International Cancer Genome Consortium; ROC, receiver operating characteristic; DDX55, DEAD-box helicase 55; RAB10, RAB10, member RAS oncogene family; RAB7A, RAB7A, member RAS oncogene family; TAF1B, TATA-box binding protein associated factor, RNA polymerase I subunit B; TAF3, TATA-box binding protein associated factor 3; AUC, area under the curve.

Article Snippet: The following antibodies were used: β-actin (1:1,000; cat. no. ET1702-52; HUABIO), DDX55 (1:1,000; cat. no. ER63225; HUABIO), RAB10 (1:1,000; cat. no. 11808-1-AP; Proteintech Group, Inc.), RAB7A (1:1,500; cat. no. 55469-1-AP; Proteintech Group, Inc.), TAF1B (1:500; cat. no. 12818-1-AP; Proteintech Group, Inc.), FOXO3 (1:1,000; cat. no. A9270; ABclonal Biotech Co., Ltd.) and TAF3 (1:500; cat. no. 18901-1-AP; Proteintech Group, Inc.), HRP conjugated goat anti-rabbit IgG polyclonal antibody (1:30000, HA1001, HUABIO), HRP conjugated goat anti-mouse IgG polyclonal antibody (1:30,000, HA1006, HUABIO).

Techniques: Biomarker Discovery, Expressing, Binding Assay

Journal: Oncology Letters

Article Title: Identification of a novel FOXO3‑associated prognostic model in hepatocellular carcinoma

doi: 10.3892/ol.2025.14976

Figure Lengend Snippet: Identification of five biomarkers in HCC. (A) mRNA expression of DDX55, RAB10, RAB7A, TAF1B and TAF3 in HCC and normal tissues from TCGA. Overall survival curves in patients with HCC with high or low expression of (B) DDX55, (C) RAB10, (D) RAB7A, (E) TAF1B and (F) TAF3 from TCGA dataset. The best cut-off value for each gene was obtained using the X-tile software. (G) mRNA expression of DDX55, RAB10, RAB7A, TAF1B and TAF3 in HCC and paired paracancerous tissues from 10 patients with HCC, assessed using reverse transcription-quantitative PCR. (H) Immunohistochemical images of DDX55, RAB10 and RAB7A in HCC and normal tissues obtained from the HPA. (I) Protein expression of DDX55, RAB10, RAB7A, TAF1B and TAF3 in HCC and paired paracancerous tissues from 10 patients with HCC, evaluated using western blot analysis. The figure on the right is a relative semi-quantitative histogram of protein expression. The gray values were obtained by ImageJ and analyzed using GraphPad Prism. (J) Cell Counting Kit-8 curves after knockdown of RAB10, RAB7A and TAF3 in Huh7 cells by siRNA. *P<0.05; **P<0.01; ***P<0.001; ****P<0.0001. T, tumor; NT, not-tumor; HCC, hepatocellular carcinoma; TCGA, The Cancer Genome Atlas; DDX55, DEAD-box helicase 55; RAB10, RAB10, member RAS oncogene family; RAB7A, RAB7A, member RAS oncogene family; TAF1B, TATA-box binding protein associated factor, RNA polymerase I subunit B; TAF3, TATA-box binding protein associated factor 3; HPA, The Human Protein Atlas; NC, negative control.

Article Snippet: The following antibodies were used: β-actin (1:1,000; cat. no. ET1702-52; HUABIO), DDX55 (1:1,000; cat. no. ER63225; HUABIO), RAB10 (1:1,000; cat. no. 11808-1-AP; Proteintech Group, Inc.), RAB7A (1:1,500; cat. no. 55469-1-AP; Proteintech Group, Inc.), TAF1B (1:500; cat. no. 12818-1-AP; Proteintech Group, Inc.), FOXO3 (1:1,000; cat. no. A9270; ABclonal Biotech Co., Ltd.) and TAF3 (1:500; cat. no. 18901-1-AP; Proteintech Group, Inc.), HRP conjugated goat anti-rabbit IgG polyclonal antibody (1:30000, HA1001, HUABIO), HRP conjugated goat anti-mouse IgG polyclonal antibody (1:30,000, HA1006, HUABIO).

Techniques: Expressing, Software, Reverse Transcription, Real-time Polymerase Chain Reaction, Immunohistochemical staining, Western Blot, Cell Counting, Knockdown, Binding Assay, Negative Control

Journal: bioRxiv

Article Title: TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing

doi: 10.1101/2024.02.05.578926

Figure Lengend Snippet: (A) Live-cell confocal microscopy (AiryScan) images of HeLa cells expressing a GFP-tagged simian virus 40 (SV40) nuclear localization signal (NLS). Single confocal planes are shown. DNA was stained with Hoechst 33342. Scale bars, 5 µm and 1 µm (inset). (B) Immunoblot of whole-cell lysates from HeLa cells imaged in . Protein expression was induced for 20 h with doxycycline (Dox). GFP–TAF1 and GFP–TAF3 expression was not detected and thus immunoblotted separately. Filled circles indicate bands corresponding to the expected molecular weight of the GFP-fusion proteins. Uncropped images can be found in the source data related to .

Article Snippet: Antibodies used were mouse monoclonal anti-sc35/SRRM2 (Sigma, S4045, 1:2,000), rabbit polyclonal anti-RBM25 (Sigma, HPA070713, 1:200), rabbit polyclonal anti-RBM14 (Sigma, HPA006628, 1:50), rabbit monoclonal anti-TAF1 (in-house/Abcam, cTAF1 177-4 )1:100), TAF3 (Abcam, ab188332, 1:500), MED1 (Abcam, ab64965, 1:500) and rabbit polyclonal anti-TAF2 (pAb 3038 , 1:100).

Techniques: Confocal Microscopy, Expressing, Virus, Staining, Western Blot, Molecular Weight

Journal: bioRxiv

Article Title: TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing

doi: 10.1101/2024.02.05.578926

Figure Lengend Snippet: (A) Fixed-cell confocal microscopy (AiryScan) images of HeLa cells expressing the individual TFIID subunits of the 3TAF complex (TAF2, TAF8, and TAF10) as GFP-fusions. Cells are stained with the nuclear speckle marker sc35. Maximum intensity projections from Z-stacks are shown. See also . (B) Fluorescence intensity profiles along the dashed lines in the insets in (A) . (C) Fixed-cell confocal microscopy (AiryScan) images of the HeLa GFP–TAF2 cell line stained with antibodies directed against endogenous RBM14 (paraspeckle marker), TAF1, TAF3, and MED1 (Mediator subunit 1). White arrow heads point at paraspeckles lying adjacent to nuclear speckles. Maximum intensity projections from Z-stacks are shown. (D) Fluorescence intensity profiles along the dashed lines in the insets in (C) . (E) Fixed-cell confocal microscopy (AiryScan) images of human HeLa and U2OS cells. Single confocal planes are shown. (F) Schematic of the experimental strategy for proximity biotinylation using miniTurbo-tagged proteins. (G) Relative abundances of TFIID subunits and RNA-binding proteins from proximity biotinylation experiments. HeLa nuclear extracts expressing miniTurbo-tagged TAF2 and TAF4 were subjected to streptavidin or control pulldowns and analyzed by label-free quantitative mass spectrometry (MS). TFIID subunits and the top 20 miniTurbo–TAF2 RNA-binding protein interactors (according to t -test difference, Supplemental table S1), in addition to nuclear speckle proteins SRRM2 and SON are shown. Normalized iBAQ values are plotted as mean ± s.d. of technical triplicates.

Article Snippet: Antibodies used were mouse monoclonal anti-sc35/SRRM2 (Sigma, S4045, 1:2,000), rabbit polyclonal anti-RBM25 (Sigma, HPA070713, 1:200), rabbit polyclonal anti-RBM14 (Sigma, HPA006628, 1:50), rabbit monoclonal anti-TAF1 (in-house/Abcam, cTAF1 177-4 )1:100), TAF3 (Abcam, ab188332, 1:500), MED1 (Abcam, ab64965, 1:500) and rabbit polyclonal anti-TAF2 (pAb 3038 , 1:100).

Techniques: Confocal Microscopy, Expressing, Staining, Marker, Fluorescence, RNA Binding Assay, Mass Spectrometry

Journal: Nature Communications

Article Title: Release of Histone H3K4-reading transcription factors from chromosomes in mitosis is independent of adjacent H3 phosphorylation

doi: 10.1038/s41467-023-43115-3

Figure Lengend Snippet: A In vitro kinase assay of recombinant human Haspin using recombinant nucleosomes with the indicated modifications as substrates ( n = 3). *** p < 0.0001, * p = 0.0035, using a mixed effects model with Dunnett’s adjustments for multiple comparisons, when compared to phosphorylation in the absence of peptide. B Phosphorylation of modified H3 peptides driven by mitotic HeLa cell extracts ( n = 3). *** p < 0.0001, * p = 0.0058, using a repeated measures two-way ANOVA with Dunnett’s adjustment for multiple comparisons, when compared to phosphorylation in the absence of peptide. C Phosphorylation of modified H3 peptides driven by mitotic HeLa cell extracts in the presence and absence of 10 µM Haspin inhibitor 5-iodotubercidin (5-Iodo) ( n = 4). *** p < 0.0001 using a repeated measures one-way ANOVA with Dunnett’s adjustment for multiple comparisons, when compared to phosphorylation in the absence of peptide. Bars represent mean ± SD; n refers to the number of independent kinase assays. All statistical analyses were carried out using non-normalized data. Source data including exact p values are provided as a Source Data file.

Article Snippet: Plasmids encoding recombinant WT (RRID:Addgene_92100) and M880A mutant human GST-TAF3-PHD were kindly provided by Albert Jeltsch .

Techniques: In Vitro, Kinase Assay, Recombinant, Phospho-proteomics, Modification